Contacts of the strand formed by residues 30 - 34 (chain P) in PDB entry 2BDI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 30 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P GLN* 3.0 19.4 + - - +
28P PRO 4.3 2.9 - - - +
29P TRP* 1.3 82.1 - - - +
31P ALA* 1.3 60.9 + - - +
32P ALA 4.4 0.2 + - - -
43P SER* 3.5 18.5 + - - -
44P GLY 3.9 2.5 - - - -
66P GLY 4.1 4.0 - - - +
67P LEU* 3.9 14.8 - - - +
69P GLY 4.4 4.0 + - - -
70P LEU 5.2 4.0 + - - +
139P SER* 2.8 41.4 + - - +
140P GLY* 3.7 0.3 - - - -
141P TRP* 3.6 27.0 - - + -
155P LEU* 3.4 23.4 - - + +
198P PRO* 3.1 26.8 - - - +
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Residues in contact with ALA 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P TRP 4.3 2.0 - - - +
30P GLN* 1.3 73.8 - - - +
32P ALA* 1.3 59.8 + - - +
33P LEU* 4.5 1.1 - - + -
43P SER* 3.0 10.9 + - - -
44P GLY* 2.7 53.4 + - - +
45P VAL* 4.3 0.7 - - - +
46P LEU 4.8 0.2 - - - +
52P VAL* 4.2 12.6 - - + -
65P ILE* 4.0 19.5 - - + -
66P GLY 3.7 4.5 - - - -
67P LEU* 4.0 9.9 - - + -
141P TRP* 4.4 3.1 - - - -
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Residues in contact with ALA 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ALA* 1.3 71.9 - - - +
33P LEU* 1.4 64.2 + - - +
34P VAL* 4.0 4.5 - - + -
40P LEU* 3.8 11.7 - - + -
42P CYS 3.9 3.4 - - - -
64P THR 3.7 1.2 - - - +
65P ILE* 3.2 7.3 - - - -
66P GLY 2.9 38.8 + - - +
70P LEU* 4.1 12.3 - - + -
73P LEU* 4.8 4.9 - - + -
141P TRP* 3.6 29.5 - - + -
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Residues in contact with LEU 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ALA* 3.9 16.4 - - + +
32P ALA* 1.4 80.0 - - - +
34P VAL* 1.3 61.4 + - - +
40P LEU* 3.1 4.9 - - - +
41P PHE* 3.0 48.9 + - + -
42P CYS* 2.8 33.1 + - + +
43P SER 3.9 8.5 - - - +
44P GLY* 4.0 3.4 - - - +
52P VAL* 5.0 3.4 - - + -
54P SER* 4.2 15.3 - - - +
58P CYS* 4.5 4.7 - - + -
63P TYR* 4.4 9.9 - - + -
64P THR 4.2 2.9 - - - +
65P ILE* 4.2 19.1 - - + -
106P ILE* 4.2 18.6 - - + -
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Residues in contact with VAL 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA* 5.1 6.1 - - + +
33P LEU* 1.3 76.5 - - - +
35P MET* 1.3 64.6 + - - +
37P ASN* 5.1 2.0 - - - -
38P GLU* 3.1 19.7 - - - +
40P LEU* 3.7 20.0 - - + +
41P PHE* 3.7 6.7 - - - -
63P TYR* 5.2 1.0 - - - -
64P THR* 3.2 50.5 + - + +
66P GLY 5.8 0.4 - - - +
73P LEU* 5.5 6.3 - - + -
82P MET* 4.8 16.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il